In this study, the phylogeny ofAlburnusgenus distributed in Turkish freshwaters was performed by analyzing mitochondrial cytbgene (1141 bp) and COI gene (1551 bp) sequences from 1172 samples representing 112 populations of 24 species through their geographical distribution. According to our findings, 20 valid species are distributed in Turkey of which 18 have already been known. While sixAlburnusspecies (A. battalgilae, A. istanbulensis, A. carinatus, A. schischkovi, A. nasreddini ve A. adanensis) have been synonomized, two new species (Alburnussp.1 andAlburnussp.2) from Dicle River and capraz Stream/Susurluk River have been identified. Extinct species such asA.akiliandA. nicaeensishave not been observedin situ. Phylogenetic tree topologies and haplotype network of the 119 cytband 80 COI haplotypes detected inAlburnusspecies have indicated a consensus tree topology containing twenty lineages, each of corresponding to one species, and threeAlburnushaplogroups corresponding to the geographical origins: Eastern Anatolia (I), Mediterranean (2) and Western & Northern Anatolia (3). The results indicate that the divergence between those haplogroups may have occurred during the Middle Miocene-Middle Pleistocene periods (from 14.9 to 5.29 million years).